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Crystal structure of InhA:01 TCR in complex with HLA-E (Y84C) bound to InhA (53-61 GCG)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5W1W 5W1W, 5EU6 experimental model PDB 5EU6 5W1W, 5EU6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293.15 0.1 M Tris pH 8.5, 25% (w/v) PEG 4000, 15% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.46 49.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.87 α = 90 b = 107.86 β = 90 c = 119.04 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2018-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.17 79.93 99.31 0.102 0.04 0.999 12.8 7.3 49326
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.21 98.89 1.342 0.579 0.581 1.2 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5W1W, 5EU6 2.17 79.93 46900 2369 99.2 0.21081 0.20908 0.2163 0.24419 0.245 RANDOM 45.68
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 4.5 -1.48 -3.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.566 r_dihedral_angle_1_deg 17.43 r_dihedral_angle_4_deg 14.806 r_dihedral_angle_3_deg 13.684 r_long_range_B_refined 3.847 r_long_range_B_other 3.821 r_mcangle_it 2.312 r_mcangle_other 2.311 r_scangle_other 2.04 r_mcbond_it 1.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.566 r_dihedral_angle_1_deg 17.43 r_dihedral_angle_4_deg 14.806 r_dihedral_angle_3_deg 13.684 r_long_range_B_refined 3.847 r_long_range_B_other 3.821 r_mcangle_it 2.312 r_mcangle_other 2.311 r_scangle_other 2.04 r_mcbond_it 1.323 r_mcbond_other 1.323 r_scbond_it 1.205 r_scbond_other 1.205 r_angle_refined_deg 1.175 r_angle_other_deg 1.08 r_chiral_restr 0.036 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6522 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing